Biomedical subjects

Jerzy Tyszkiewicz

Publications and source records attributed to Jerzy Tyszkiewicz.

3 recordsLinked to original sources

PubMed2006

XQTav: an XQuery processor for Taverna environment.

UNLABELLED: Taverna workbench is an environment for construction, visualization and execution of bioinformatic workflows that integrate specialized tools available through the internet. It is gaining popularity fast, because of supporting the most important bioinformatic services and its simple, yet robust graphical notation. Here we present XQTav-an extension of Taverna that provides full integration with XQuery (the query language for XML) engine. XQTav allows execution of XQuery scripts in Taverna workflow diagrams. All existing Taverna processors can be accessed in the XQuery scripts. This provides an alternative way of specifying subworkflows in Taverna and is useful when one deals with query-like algorithms (e.g. filters and inner joins). Moreover, XQtav may be used to automatically generate an XQuery script that is equivalent to Taverna's workflow. This constitutes another way of creating and enacting bioinformatic workflows: overall structure of a diagram is drawn in Taverna environment, XQuery code is generated and possibly adjusted by hand. It can be executed by XQuery engines or incorporated into other software environments. AVAILABILITY: XQtav is an open source software. It may be downloaded from http://xqtav.sourceforge.net/. The page also contains various tutorials and examples, including the one described in this report.

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PubMed2002

Contextual alignment of biological sequences (Extended abstract).

We present a model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which we assume that the cost of a substitution depends on the surrounding symbols. In this model the cost of transforming one sequence into another depends on the order of editing operations. We present efficient algorithms for calculating this cost, as well as reconstructing (the representation of) all the orders of operations which yield this optimal cost. A precise characterization of the families of linear orders which can emerge this way is given.

Algorithms↗

PubMedDate not supplied

Alignment with context dependent scoring function.

In the paper by Gambin et al. (2002) we introduced the model of contextual alignment of biological sequences. It is an extension of the classical alignment, in which the cost of a substitution depends on the surrounding symbols. Consequently, in this model the cost of transforming one sequence into another depends on the order of editing operations. In this paper, we strengthen some of our results which concern reconstructing (the representation of) all the orders of operations which yield this optimal cost. We also present a procedure to construct context-dependent substitution tables and discuss the distribution of scores of local contextual alignment, which is shown to follow the extreme value distribution in the gap-free, reduced context case. We also demonstrate a linear time algorithm to compute the optimal local and global alignment without gaps.

Algorithms↗